Sea-level changes and palaeo-ranges: reconstruction of ancient shorelines and river drainages and the phylogeography of the Australian land crayfish Engaeus sericatus Clark (Decapoda: Parastacidae )

Historical sea levels have been influential in shaping the phylogeography of freshwater-limited taxa via palaeodrainage and palaeoshoreline connections. In this study, we demonstrate an approach to phylogeographic analysis incorporating historical sea-level information in a nested clade phylogeographic analysis (NCPA) framework, using burrowing freshwater crayfish as the model organism. Our study area focuses on the Bass Strait region of southeastern Australia, which is marine region encompassing a shallow seabed that has emerged as a land bridge during glacial cycles connecting mainland Australia and Tasmania. Bathymetric data were analysed using Geographical Information Systems (GIS) to delineate a palaeodrainage model when the palaeocoastline was 150 m below present-day sea level. Such sea levels occurred at least twice in the past 500 000 years, perhaps more often or of larger magnitude within the last 10 million years, linking Victoria and Tasmania. Inter-locality distance measures confined to the palaeodrainage network were incorporated into an NCPA of crayfish (Engaeus sericatus Clark 1936) mitochondrial 16S rDNA haplotypes. The results were then compared to NCPAs using present-day river drainages and traditional great-circle distance measures. NCPA inferences were cross-examined using frequentist and Bayesian procedures in the context of geomorphological and historical sea-level data. We found distribution of present-day genetic variation in E. sericatus to be partly explained not only by connectivity through palaeodrainages but also via present-day drainages or overland (great circle) routes. We recommend that future studies consider all three of these distance measures, especially for studies of coastally distributed species.

Habitat selection by female Australian fur seals (Arctocephalus pusillus doriferus)

1. Numerous studies have determined the foraging areas of marine apex predators and investigated their relationship to oceanographic features. Most of these, however, have concentrated on surface-feeding seabirds or epipelagic-foraging marine mammals and there is little information on habitat selection in benthic divers.

2. Satellite telemetry was used during the winters of 2001-2003 to determine the foraging areas of 48 female Australian fur seals (Arctocephalus pusillus doriferus) from four breeding sites in northern Bass Strait whose colonies together represent > 80% of the total species population.

3. All individuals foraged over the shallow continental shelf of Bass Strait supporting earlier studies that suggested the species is an exclusively benthic forager. Individual females showed a high degree of foraging site-fidelity and several foraging 'hot spot' areas could be identified.

4. Analysis of habitat use indicated that individuals selected areas with depths of 60-80 m significantly more (λ = 0.216, P<0.001) than any other bathymetric class. There was also evidence for foraging areas being influenced by SST, with individuals selecting regions of 16.0-16.8 C SST (λ = 0.008, P<0.01), but not surface chlorophyll-a concentration (P> 0.05).

5. Temporal analysis of at-sea movements indicated, due to their primarily benthic foraging mode, the areas frequented by female Australian fur seals did not overlap substantially with areas targeted by commercial fisheries. An exception to this was in far eastern Bass Strait where the Otter Trawl component of the Commonwealth Trawl Sector is highly active over the continental shelf and encompasses the areas frequented by females from The Skerries colony.

Hydro-acoustic remote sensing of benthic biological communities on the shallow South East Australian continental shelf

Information regarding the composition and extent of benthic habitats on the South East Australian continental shelf is limited. In this habitat mapping study, multibeam echosounder (MBES) data are integrated with precisely geo-referenced video ground-truth data to quantify benthic biotic communities at Cape Nelson, Victoria, Australia. Using an automated decision tree classification approach, 5 representative biotic groups defined from video analysis were related to hydro-acoustically derived variables in the Cape Nelson survey area. Using a combination of multibeam bathymetry, backscatter and derivative products produced highest overall accuracy (87%) and kappa statistic (0.83). This study demonstrates that decision tree classifiers are capable of integrating variable data types for mapping distributions of benthic biological assemblages, which are important in maintaining biodiversity and other system services in the marine environment.

Rearing juvenile Australian native percichthyid fish in fertilised earthen ponds

The post-larvae and fry of Australian native species, including those of species belonging to the family Percichthyidae, are routinely reared to a fingerling size (35-55 mm in length) in fertilised earthen fry rearing ponds. The juveniles of Murray cod (Maccullochella peelii peelii\ trout cod (Maccullochella macquariensis) and Macquarie perch (Macquaria australasicd) (Percichthyidae) are grown in fry rearing ponds at the Marine and Freshwater Resources Institute, Snobs Creek (Vie. Australia) for production of fingerlings for stock enhancement and aquaculture purposes. However, no detailed studies have been undertaken of the productivity of these ponds and factors that influence fish production. An ecologically based study was undertaken to increase the knowledge of pond ecology and dynamics, particularly in relation to the rearing of juvenile Murray cod, trout cod and Macquarie perch in ponds. Over nine consecutive seasons commencing in 1991, water chemistry, plankton, macrobenthos (2 seasons only) and fish were monitored and studied in five ponds located at Snobs Creek. A total of 80 pond fillings were undertaken during the study period. Additional data collected from another 24 pond fillings undertaken at Snobs Creek collected prior to this study were included in some analyses. Water chemistry parameters monitored in the ponds included, temperature, dissolved oxygen pH, ammonia, nitrite, nitrate, orthophosphate and alkalinity. Water chemistry varied spatially (within and between ponds) and temporally (diurnally, daily and seasonally). Liming of ponds increased the total alkalinity to levels that were considered to be suitable for enhancing plankton communities and fish production. Water quality within the ponds for the most part was suitable for the rearing of juvenile Murray cod, trout cod and Macquarie perch, as reflected in overall production (growth, survival and yield) from the ponds. However, at times some parameters reached levels which may have stressed fish and reduced growth and survival, in particular, low dissolved oxygen concentrations (minimum 1.18 mg/L), high temperatures (maximum 34°C), high pH (maximum 10.38) and high unionised ammonia (maximum 0.58 mg/L). Species belonging to 37 phytoplankton, 45 zooplankton and 17 chironomid taxa were identified from the ponds during the study. In addition, an extensive checklist of aquatic flora and fauna, recorded from aquaculture ponds in south-eastern Australia, was compiled. However, plankton and benthos samples were usually numerically dominated by a few species only. Rotifers (especially Filinia, Brachionus, Polyarthra, and Asplanchnd), cladocerans (Moina and Daphnid) and copepods (Mesocyclops and Boeckelld) were most abundant and common in the plankton, while chironomids (Chironomus, Polypedilum, and Prodadius) and oligochaetes were most common and abundant in the benthos. Both abundance and species composition of the plankton and macrobenthos varied spatially (within and between ponds) and temporally (diurnally, daily and seasonally). Chlorophyll a concentrations, which ranged from 1.8 to 184 \ig/L (mean 29.37 ng/L), initially peaked within two weeks of filling and fertilising the ponds. Zooplankton peaked in abundance 2-4 weeks after filling the ponds. The maximum zooplankton density recorded in the ponds was 6,621 ind./L (mean 721 ind./L). Typically, amongst the zooplankton, rotifers were first to develop high densities (2nd-3rd week after filling), followed by cladocerans (2nd-4th week after filling) then copepods (2nd-5th week after filling). Chironomid abundance on average peaked later (during the 5th week after filling). The maximum chironomid density recorded in the ponds was 27,470 ind./m2 (mean 4,379 ind./m2). Length-weight, age-weight and age-length relationships were determined for juvenile Murray cod, trout cod and Macquarie perch reared in ponds. These relationships were most similar for Murray cod and trout cod, which are more closely related phylogenetically and similar morphologically than Macquarie perch. Growth of fish was negatively correlated with both size at stocking and stocking biomass. Stocking density experiments showed that, at higher densities, growth offish was significantly reduced, but survival was not affected. The diets of juvenile Murray cod trout cod and Macquarie perch reared in fry ponds were similar. The cladocerans Moina and Daphnia, adult calanoid and cyclopoid copepods and the chironomids, Chironomus, Polypedilum and Procladius were the most commonly occurring and abundant prey. Selection for rotifers and copepod nauplii was strongly negative for all three species of fish. Size range of prey consumed was positively correlated with fish size for trout cod and Macquarie perch, but not for Murray cod. Diet composition changed as the fish grew. Early after stocking the fish into the ponds, Moina was generally the more common prey consumed, while in latter weeks, copepods and chironomids became more abundant and common in the diet. On a dry weight basis, chironomid larvae were the most important component in the diets of these fish species. Selective feeding by fish on larger planktonic species such as adult copepods and cladocerans, may have influenced the plankton community structure as proposed by the trophic cascade or top -down hypothesis. The proximate composition and energy content of Murray cod, trout cod and Macquarie perch, reared in the ponds did not vary significantly between the species, and few significant changes were observed as the fish grew. These results suggested that the nutrient requirements of these species might not vary over the size range of fish examined. Significant differences in the proximate composition of prey were observed between species, size of species and time of season. The energy content of prey (cladocerans, copepods and chironomids) on a pond basis, was closely related to the abundance of these taxa in the ponds. Data collected from all pond fillings during the present study, along with historical data from pond fillings undertaken prior to this study, were combined in a data matrix and analysed for interactions between pairs of parameters. In particular, interactions between selected water chemistry parameters, zooplankton and chironomid abundance indicators were analysed to identify key factors that influence fish production (growth, survival, condition and yield). Significant correlations were detected between fish production indicators and several water chemistry and biota (zooplankton and chironomids) parameters. However, these were not consistent across all three species of fish. These results indicated that the interactions between water chemistry, biota and fish were complex, and that combinations of these parameters, along with other factors not included in the present study, may influence fish production in these ponds. The present study, showed that more stringent monitoring of fry rearing ponds, especially water quality, zooplankton and benthos communities and fish, combined with an associated increase in understanding of the pond ecosystem, can lead to substantial improvements in pond productivity and associated fish production. In the present study this has resulted in a general increase in fish survival rates, which became less variable or more predictable in nature. The value of such knowledge can provide managers with a more predicative capacity to estimate production of ponds in support of stock enhancement programs and provision of juvenile for aquaculture grow-out.

Crisis of meanings : divergent experiences and perceptions of the marine environment in Victoria, Australia

The oceans of the world are regularly depicted as under threat from human exploitation with the problem portrayed as being of 'global' concern. In a world market characterised by the division of labour, many of those who eat fish do so without directly experiencing the ocean as a domain of productive utility. Rather, their encounters are with representations that depict the 'natural' world as an aesthetic object of contemplation, and environmentalist discourses that identify human activities as' threatening marine ecosystems. So prevalent is this experience that tangible institutions, such as state fisheries management bodies, have emerged, acting to reinforce the ontology of this 'contemplated' ocean, giving weight to the illusion that humans can, and should, appreciate it only from afar. In this representation, commercial fishers are regularly depicted as transgressing a 'natural' boundary between humans and the environment. It is when the world is simultaneously encountered as an object of consumptive utility and aesthetic utility that the human role in the environment becomes ambiguous and a sense of crisis arises. This paper investigates disjunctions in experiences and understandings that contribute to environmental anxiety, and debates over the appropriate use of the ocean.

Deployment of DGT units in marine waters to assess the environmental risk from a deep sea tailings outfall

Measurements of total, filterable and DGT-labile concentrations of nine metals (Al, Cd, Cr, Cu, Fe, Pb, Mn, Ni and Zn) have been made at five sites up to 4.2km from a deep sea tailings outfall operated by Lihir Gold Ltd. at Lihir Island, Papua New Guinea. At each site, pairs of DGT units (one containing a 0.4mm and the other a 0.8mm diffusive gel layer) were deployed at three depths (50–70; 105–130; 135–155m) for 4–7 days. Comparison of predicted water column DGT-labile metal concentrations in field deployments showed the 0.8mm DGT units were relatively enriched in metals, with the effect being greatest closer to the outfall for Pb and Mn and least for Fe, Cr, Ni and Zn. The most likely explanation for this is that in addition to simple ion diffusion, kinetic factors associated with ageing or desorption processes govern release of metals from iron and aluminium oxyhydroxide colloids which diffuse through the gels. The thicker gels have a longer residence time over which metals can be released for adsorption. This model explains why enrichment is most pronounced near the outfall; more distant sites have lower colloid concentrations because of the longer time for coagulation to increase particle sizes to the extent they cannot enter the gels. Total and filterable metal (FM) concentrations were frequently below the limits of detection (LOD) achievable by conventional ICP-AES (1–52gL⁻¹) and this limited their usefulness for assessing environmental risk and for metal speciation determination. Because of its pre-concentration step DGT gave metal concentrations above their LODs and these decreased exponentially with distance from the outfall. Concentrations of DGT–labile metal fell below Australian water quality guidelines for protection of 99% of marine organisms within 0.13km of the outfall for Cd, Cr and Ni and below that for protection of 95% of marine organisms within 0.4, 0.7 and 3.6km for lead, zinc and copper, respectively.

Mislabeling marine protected areas and why it matters : a case study of Australia

As part of international obligations and national policies, most nations are working toward establishing comprehensive, adequate, and representative systems of terrestrial and marine protected areas (MPAs). Assigning internationally recognized International Union for Conservation of Nature (IUCN) protected area categories to these MPAs is an important part of this process. The most recent guidance from the IUCN clearly states that commercial or recreational fishing is inappropriate in MPAs designated as category II (National Park). However, in at least two developed countries with long histories of protected area development (e.g., Canada and Australia), category II is being assigned to a number of MPAs that allow some form of commercial or recreational fishing. Using Australia as a case study, this article explores the legal and policy implications of applying protected area categories to MPAs and the consequences for misapplying them. As the Australian Government is about to embark on potentially one of the largest expansions of MPA networks in the world, ensuring the application of IUCN categories is both transparent and consistent with international practice will be important, both for the sake of international conventions and to accurately track conservation progress.

Epizootiology of brucella infection in Australian fur seals

Novel members of the bacterial genus Brucella have recently emerged as pathogens of various marine mammal species and as potential zoonotic agents. We investigated the epizootiology of Brucella infection in Australian fur seals (Arctocephalus pusillus doriferus) by establishing demographic and temporal variations in antibody prevalence, attempting isolation of the causative agent, and determining whether this potential pathogen is involved in frequent abortions observed in this pinniped species. Two competitive enzyme-linked immunosorbent assays (cELISAs), an indirect ELISA, and a fluorescence polarization assay (FPA) were used to test sera for Brucella antibodies. The FPA and cELISA proved suitable for use in this species. Significant differences in antibody prevalence were found between age classes of seals sampled between 2007 and 2009 at one colony. Pups sampled at this site (n5134) were negative for Brucella antibodies by all serologic tests but 17 of 45 (38%) of juveniles were antibody-positive. Antibody prevalence in adult females was significantly higher than in juveniles (P50.044). Antibody prevalence for adult females between 2003 and 2009 varied significantly over time (P50.011), and for individuals sampled between 2003 and 2005, the likelihood of pregnancy was greater in individuals positive for Brucella antibodies (P50.034). Inflammatory lesions suggestive of infectious agents were found in 14 of 39 aborted Australian fur seal pups, but pathologic changes were not uniformly consistent for Brucella infection. Culture and PCR investigations on fetal tissues were negative for Brucella. Culture and PCR on selected fresh or frozen tissues from 36 juvenile and adult animals were also negative. We suspect that the prevalence of active infection with Brucella in Australian fur seals is low relative to antibody prevalence. © Wildlife Disease Association 2011.

Stable isotopes reveal inter-annual and inter-individual variation in the diet of female Australian fur seals

Understanding the temporal and spatial variation of foraging habits of apex predators is central to understanding their role in marine ecosystems and how their populations may respond to environmental variability. In the present study, stable isotope analysis (C and N) of blood was used to investigate inter-individual and inter-annual differences in the diet of adult female Australian fur seals Arctocephalus pusillus doriferus. Positive correlations were observed between red cell and plasma values for δ¹³C and δ¹⁵N (r² = 0.47 and r² = 0.66, respectively, p < 0.001 in both cases), suggesting relatively consistent individual prey choices over 3 or 4 foraging trips. Mean δ¹⁵N values (12.8 to 17.5%) confirm the species occupies the highest marine trophic niche in the region. A significant decrease in plasma δ¹⁵N values, corresponding to two-thirds of a trophic level (ca. 2%), was observed between the 1998 to 2000 and 2003 to 2005 sampling periods. This was associated with a significant decrease in adult female body condition and is consistent with a decline, previously documented by faecal analysis, of the proportion of red cod Pseudophysis bachus, barracouta Thyrsites atun and Gould's squid Nototodarus gouldi in the diet and an increase in redbait Emmelichthys nitidus. While substantial variation in δ¹⁵N was observed within each age cohort, a significant decrease was observed with age, suggesting individual specialisation for particular prey types is evident early in adulthood, but that its composition changes as females age. In addition, generalized linear models indicated body mass had a negative influence on δ¹⁵N, which may reflect larger total body oxygen stores, facilitating individuals hunting cryptic prey of lower trophic level (e.g. octopus) on the sea floor.

Field evaluation of a suite of biomarkers in an Australian Tropical Reef Species, Stripey Seaperch (Lutjanus carponotatus) : Assessment of Produced Formation water from the Harriet A Platform

There is paucity of data regarding hydrocarbon exposure of tropical fish species inhabiting the waters near oil and gas platforms on the Northwest Shelf of Australia. A comprehensive field study assessed the exposure and potential effects associated with the produced water (PW) plume from the Harriet A production platform on the northwest shelf in a local reef species, Stripey seaperch (Lutjanus carponotatus). This field study was a continuation of an earlier pilot study which concluded that there were “warning signs” of potential biological effects on fish populations exposed to PW. A 10-day field caging study was conducted deploying 15 individual fish into 6 separate steel cages set 1-m subsurface at 3 stations in a concentration gradient moving away from the platform. A battery of biomarkers were evaluated including hepatosomatic index (HSI), total cytochrome P450, bile metabolites, CYP1A-, CYP2K- and CYP2M-like proteins, cholinesterase (ChE) activity, and histopathology of liver and gill tissues. Water column and PW effluent samples was also collected. Results confirmed that PAH metabolites in bile, CYP1A-, CYP2K-, and CYP2M-like proteins and liver histopathology provided evidence of significant exposure and effects after 10 days at the near-field site (~200 m off the Harriet A platform). Hepatosomatic index, total cytochrome P450, and ChE did not provide site-specific differences by day 10 of exposure to PW. CYP proteins were shown by principal component analysis (PCA) to be the best diagnostic tool for determining exposure and associated biological effects of PW on L. carponotatus. Using a suite of biomarkers has been widely advocated as a vital component in environmental risk assessments worldwide. This study demonstrates the usefulness of biomarkers for assessing the Harriet A PW discharge into Australian waters with broader applications for other PW discharges. This approach has merit as a valuable addition to environmental management strategies for protecting Australia’s tropical environment and its rich biodiversity.

Foraging trip strategies and habitat use during late pup rearing by lactating Australian fur seals

Australian fur seals (Arctocephalus pusillus doriferus) are the most conspicuous and abundant marine mammal in shelf waters of south-eastern Australia. To successfully rear offspring, the females must encounter sufficient prey on each foraging trip out of a central place for periods up to11 months each year. We investigated foraging trip strategies and habitat use by the females in three winter–spring periods, 2001–03, from four colonies that span the species’ latitudinal range and contribute 80% of pup production. Trip durations of 37 females averaged 6.1±0.5 (s.e.) days, although >90% of the seal’s time at sea was spent <150 km travel (<2 days) away. Most females exhibited strong fidelities to individually preferred hotspots Females from colonies adjacent to productive shelf-edge waters generally had shorter trips, had smaller ranges, foraged closer to colonies and exhibited less diversity in trip strategies than did those from colonies more distant from a shelf-edge. From a management perspective, there was minimal overlap (<1%) between where females foraged and a system of marine reserves established in 2007, suggesting that habitats visited by lactating Australian fur seals currently receive minimal legislative protection

The Bassian Isthmus and the major ocean currents of southeast Australia influence the phylogeography and population structure of a southern Australian intertidal barnacle Catomerus polymerus (Darwin)

Southern Australia is currently divided into three marine biogeographical provinces based on faunal distributions and physical parameters. These regions indicate eastern and western distributions, with an overlap occurring in the Bass Strait in Victoria. However, studies indicate that the boundaries of these provinces vary depending on the species being examined, and in particular on the mode of development employed by that species, be they direct developers or planktonic larvae dispersers. Mitochondrial DNA sequence analysis of the surf barnacle Catomerus polymerus in southern Australia revealed an east–west phylogeographical split involving two highly divergent clades (cytochrome oxidase I 3.5 ± 0.76%, control region 6.7 ± 0.65%), with almost no geographical overlap. Spatial genetic structure was not detected within either clade, indicative of a relatively long-lived planktonic larval phase. Five microsatellite loci indicated that C. polymerus populations exhibit relatively high levels of genetic divergence, and fall into four subregions: eastern Australia, central Victoria, western Victoria and Tasmania, and South Australia. F_ST values between eastern Australia (from the eastern mitochondrial DNA clade) and the remaining three subregions ranged from 0.038 to 0.159, with other analyses indicating isolation by distance between the subregions of western mitochondrial origin. We suggest that the east–west division is indicative of allopatric divergence resulting from the emergence of the Bassian land-bridge during glacial maxima, preventing gene flow between these two lineages. Subsequently, contemporary ecological conditions, namely the East Australian, Leeuwin, and Zeehan currents and the geographical disjunctions at the Coorong and Ninety Mile Beach are most likely responsible for the four subregions indicated by the microsatellite data.

Ratio-dependent response of a temperate Australian estuarine system to sustained nitrogen loading

Classical resource- and the less studied ratio-dependent models of predator–prey relationships provide divergent predictions as to the sustained ecological effects of bottom-up forcing. While resource-dependent models, which consider only instantaneous prey density in modelling predator responses, predict community responses that are dependent on the number of trophic levels in a system, ratio-dependent models, which consider the number of prey per consumer, predict proportional increase in each level irrespective of chain length. The two models are only subtly different for systems with two or three trophic levels but in the case of four trophic levels, predict opposite effects of enrichment on primary producers. Despite the poor discriminatory power of tests of the models in systems with two or three trophic levels, field tests in estuarine and marine systems with four trophic levels have been notably absent. Sampling of phytoplankton, macroinvertebrates, invertebrate-feeding fishes, piscivorous fishes in Kooloonbung Creek, Hastings River estuary, eastern Australia, subject to over 20 years of sewage discharge, revealed increased abundances in all four trophic levels at the disturbed location relative to control sites. Increased abundance of phytoplankton at the disturbed site was counter to the predictions of resource-dependent models, which posit a reduction in the first trophic level in response to enrichment. By contrast, the increase in abundance of this first trophic level and the proportionality of increases in abundances of each of the four trophic groups to nitrogen loading provided strong support for ratio dependency. This first evidence of ratio dependence in an estuarine system with four trophic levels not only demonstrates the applicability of ecological theory which seeks to simplify the complexity of systems, but has implications for management. Although large nutrient inputs frequently induce mortality of invertebrates and fish, we have shown that smaller inputs may in fact enhance biomass of all trophic levels.

Changes in muscle composition during the development of diving ability in the Australian fur seal

During development the Australian fur seal transitions from a terrestrial, maternally dependent pup to an adult marine predator. Adult seals have adaptations that allow them to voluntarily dive at depth for long periods, including increased bradycardic control, increased myoglobin levels and haematocrit. To establish whether the profile of skeletal muscle also changes in line with the development of diving ability, biopsy samples were collected from the trapezius muscle of pups, juveniles and adults. The proportions of different fibre types and their oxidative capacity were determined. Only oxidative fibre types (Type I and IIa) were identified, with a significant change in proportions from pup to adult. There was no change in oxidative capacity of Type I and IIa fibres between pups and juveniles but there was a two-fold increase between juveniles and adults. Myoglobin expression increased between pups and juveniles, suggesting improved oxygen delivery, but with no increase in oxidative capacity, oxygen utilisation within the muscle may still be limited. Adult muscle had the highest oxidative capacity, suggesting that fibres are able to effectively utilise available oxygen during prolonged dives. Elevated levels of total creatine in the muscles of juveniles may act as an energy buffer when fibres are transitioning from a fast to slow fibre type.